NVT Molecular Dynamics Simulations Research Articles

Molecular dynamics simulation of diffusion of gases in pure and silica-filled poly(1-trimethylsilyl-1-propyne) [PTMSP

Nanocomposites have been extensively applied, and molecular dynamics simulation techniques have been applied to study the diffusion of gases (H2, O2, N2, CO2, CH4, n-C4H10) through pure and filled with silica particle poly(1-trimethylsilyl-1-propyne) [PTMSP]. The aim for this research is to explore and investigate the effect of silica particle on the diffusion of gases in polymer. The diffusion coefficients of gases were determined via NVT molecular dynamics simulation using the COMPASS force field up to 500 or 1000ps simulation time. We have focused on the effect of the concentration and the size of the silica particles on diffusion coefficients of gases and the changes of free volume and translational dynamics and intermolecular energies. It has been found that the addition of silica particle to PTMSP increased the diffusion coefficients of gases by enhancing the free volume of polymer.

Molecular Dynamics Study of Translational and Rotational Diffusion in Liquid Ortho-terphenyl

NVT molecular dynamics simulations were performed on liquid o-terphenyl as a function of temperature in the range 320-480 K. Computed translational diffusion coefficients displayed the non-Arrhenius behavior expected of a fragile glass-forming liquid and were in good, semiquantitative agreement with experimental results. Rotational correlation functions calculated for various vectors within the molecule exhibited a very short time (0-1 ps) initial decay, followed by a reversal, which corresponds to free reorientation within the "solvent" cage prior to collision with a wall. Rotational correlation times of three orthogonal vectors fixed on the central benzene were close to equal at all temperatures, indicating nearly isotropic overall molecular reorientation. The average correlation times exhibited a non-Arrhenius temperature dependence and were in very good agreement with experimental values derived from 2D and 1H NMR relaxation times. Correlation times of vectors located on the lateral phenyl rings were used to calculate the "spinning" internal rotation diffusion coefficients, which were approximately twice as great as the overall rotational diffusion constants, indicating rapid internal rotation of the phenyl side groups over wide ranges of angle in the liquid.

Pressure and Temperature Dependence of the Hydrogen Bonding in Supercritical Ethanol: A Computer Simulation Study

As a step toward deeper insight on the "hydrogen bonding" in supercritical ethanol (scEtOH), we carried out NVT molecular dynamics simulations of the fluid over a wide range of temperatures and pressures. The fluid was studied at SC conditions for which thermodynamic and spectroscopic (NMR, infrared, Raman, dielectric) data are available. The various site-site pair distribution functions (pdf's) were calculated, and their temperature and pressure dependence was obtained. It was found that over the thermodynamic conditions investigated here, scEtOH remains highly structured. Moreover, the characteristic behavior of the first peaks in H-H, O-O, and H-O pdf's reveals that hydrogen bonds still exist in scEtOH. The analysis focuses also on the reorientational dynamics of the bond unit vectors O-H, C-O, and of the permanent dipole moment of the molecules as well as the total dipole moment of the sample. The corresponding Legendre time correlation functions were discussed in connection to the "hydrogen bonding" in the fluid and in the context of experimental results. Specifically, the behavior of the O-H dynamics exhibits the well-known associative nature of the molecules in the system. A further analysis of the hydrogen bonds was carried out, and the degree of aggregation (average number of H-bonds per molecule) was obtained and compared with results from NMR chemical shift studies. Also the estimated monomer and free O-H groups in the fluid were compared with results from IR and Raman vibrational spectroscopy. The percentage analysis fi of the liquid and scEtOH molecules, with i = 0, 1, 2, 3, ... hydrogen bonds per molecule, has been obtained. The results show the existence of small, linear-chain oligomers formed mainly by two molecules, whereas the number of the three body oligomers, and specifically that of four body oligomers in the sample, is relatively small.

Molecular Dynamics Study of Anisotropic Translational and Rotational Diffusion in Liquid Benzene

Equilibrium NPT and NVT molecular dynamics simulations were performed on liquid benzene over an extended range of temperature (from 260 to 360 K) using the COMPASS force field. Densities and enthalpies of vaporization (from cohesive energy densities) were within 1% of experiment at all temperatures. tumbling and spinning rotational diffusion coefficients, D(perpendicular) and D(parallel), computed as a function of temperature, agreed qualitatively with the results of earlier reported experimental and computational investigations. Generally, it was found that D(parallel)/D(perpendicular) approximately 1.4-2.5 and the activation energy for tumbling was significantly greater than for spinning about the C6 axis [Ea(D(perpendicular)) = 8.1 kJ mol(-1) and Ea(D(parallel)) = 4.5 kJ mol(-1)]. Calculated translational diffusion coefficients were found to be in quantitative agreement with experimental values at all temperatures [deviations were less than the scatter between different reported measurements]. In addition, translational diffusion coefficients were computed in the molecule-fixed frame to yield values for Dxy (diffusion in the plane of the molecule) and Dz (diffusion perpendicular to the plane). It was found that the ratio Dxy/Dz approximately 2.0, and that the two coefficients have roughly equal activation energies. This represents the first atomistic molecular dynamics study of translational diffusion in the molecular frame.

Computationally designed monomers and polymers for molecular imprinting of theophylline and its derivatives. Part I

The main objective of this research was to develop and apply state-of-the-art computational tools to achieve an understanding of intermolecular interactions in molecular imprinting of theophylline into complex polymeric systems. Molecular dynamics (MD) simulations were carried out for different molecular systems in order to predict the interaction energies, the closest approach distances and the active site groups between the simulated molecular systems and different bio-ligands. The minimized structures of five ligands, theophylline and its derivatives (theobromine, theophylline-8-butanoic acid, caffeine and theophylline-7-acetic acid) have been obtained with the use of molecular mechanics approach. NVT MD simulations at room temperature were carried out to obtain equilibrated conformations in all cases. The first simulated molecular systems consisted of a ligand and a commonly used functional monomer, such as acrylic acid, methacrylic acid, acrylamide, acrolein, acrylonitrile, styrene, etc. (a total number of 25 monomers were simulated). For each of the simulated monomer, molecular clusters consisting of 10 monomers were built. For each pair of molecular systems, (10 monomers with a ligand and 10 monomers without a ligand) a total energy difference, (Δ E), was calculated in order to estimate the interaction energy between a ligand and the corresponding monomers. The second simulated molecular systems consisted of a ligand and a polymer. For each of the simulated polymers, a polymeric chain with degree of polymerization (DP) 10 was simulated with theophylline or its derivative and the interaction energy (Δ E) was calculated. From simulated polymer systems it was found that just poly(acrylic acid) and poly(itaconic acid) are selective only for theophylline. The functional groups of monomers interacting with ligands are –COOH or CH 2 CH–. The functional groups of polymers are predominantly –COOH. In the case of poly(acrylic acid) and poly(itaconic acid) the distance of closest approach between a polymer and theophylline was between 2.0 and 4.0 Å.

Computationally designed monomers and polymers for molecular imprinting of theophylline—part II

The main objective of this research is to develop and apply state-of-the-art computational tools to achieve an understanding of intermolecular interactions in molecular imprinting of theophylline into complex polymeric systems. Molecular dynamics (MD) simulations were carried out for different molecular systems in order to predict the interaction energies, the closest approach distances and the active site groups between the simulated molecular systems and different bio-ligands. The minimized structures of five ligands, theophylline and its derivatives (theobromine, theophylline-8-butanoic acid, caffeine and theophylline-7-acetic acid) have been obtained with the use of molecular mechanics approach. NVT MD simulations at room temperature were carried out to obtain equilibrated conformations in all cases. The first simulated molecular systems consisted of a ligand and commonly used functional monomers, polymers and a substrate. The second simulated molecular systems consisted of a ligand and a monomer or polymer using a solvent (ethanol). During this study, it was found that electrostatic interactions play the most significant role in the formation of molecular imprinting materials. The simulated functional monomers and polymers with ligands indicate that the functional groups interacting with ligands tends to be either –COOH or CH 2 CH–. It was also found that molecular substrate without functional side groups are recommended for molecular imprinting technology. For both the solvated monomer and polymer systems is that it appears that the presence of the solvent appears to favour the formation of more stable clusters with theophylline than with its derivatives.

Investigation of the vapor–liquid equilibrium and supercritical phase of pure methane via computer simulations

The Gibbs Ensemble Monte Carlo (GEMC) simulation technique was used to study the vapor–liquid equilibrium (VLE) of pure methane in a wide range of thermodynamic state points. The properties of the pure fluid were also studied at supercritical (SC) conditions by performing NVT and NPT molecular dynamics (MD) simulations. Previously developed intermolecular potential models were employed to model the fluid and their properties were obtained and compared with available experimental data. The simulations have shown that a simple one site Lennard–Jones (LJ) potential model [B. Saager and J. Fischer, Fluid Phase Equil. 57 (1990) 35, J. Fischer, R. Lustig, H. Breitenfelder_Manske and W. Lemming, Mol. Phys. 52 (1984) 485.] provides accurate descriptions of the VLE state points. It is also suggested that for the accurate description of the fluid properties at SC conditions, one needs to employ all-atom (AA) interaction potentials to model the system. The effectiveness of such kind of potential models used in this study has been presented and discussed.

MEAM molecular dynamics study of a gold thin film on a silicon substrate

Modified embedded atom method (MEAM) models have been used in conjunction with molecular dynamics simulations to study the interface between a silicon substrate and a thin overlayer of gold. Due to the absence of stable compound formation in the Au–Si phase diagram, we computed ground state properties for a representative Au–Si structure, namely the B1(NaCl) structure within the local density approximation (LDA), and fitted MEAM parameters to this data. The MEAM potentials were tested for their ability to reproduce LDA calculations such as the predictions of properties for Au/Si in the L1 2 structure, the binding energies and bond lengths for two isolated clusters, the energy barrier for an Au atom migrating in the (1 1 0) channel of c-Si, and some fundamental physical properties for elemental Au. All errors are within 10%. The molecular dynamics simulations focussed mainly on investigating three critical issues where experimental data conflict: (1) the critical coverage of Au atoms needed to induce intermixing at the interface, (2) the composition of the topmost layer and the surface region under different Au coverages, and (3) the influence of temperature on the chemical composition of the Au–Si interface. NVT molecular dynamics simulations at room temperature showed that the formation of silicides at the Au–Si interface is very fast and can be formed at very low coverage (0.11 monolayer). We observed a structural transition from disordered silicides at low coverage to a crystalline Au top layer as the number of monolayers increased. The thickness of the silicide layer formed at the interface initially increased rapidly but reached a constant value after a certain amount of Au atoms were deposited. The interface between an Au thin film and an Si substrate consisted of two alloyed regions separated by an 80-at.% Au-rich layer. In contrast, the interface between an Au island and an Si substrate involved a 50–50 alloy, formed near the top layer of the Si substrate. Annealing at 500 K altered the distribution of Au and Si atoms in the alloyed region, even though the average composition of the intermixed layer remained the same as that before annealing. Between 500 and 800 K, we observed rapid growth of a silicide layer and a transition from an Au-rich to an Si-rich surface region due to a dramatic increase of Si outdiffusion. Annealing to 1000 K did not alter the boundary between the Au silicide and the Si substrate, implying that Au indiffusion had diminished and the growth of Au silicides was dominated by the outdiffusion of Si atoms within this temperature range.

THE ORDER AND POLARISATION OF A SYSTEM COMPOSED OF BENT POLAR GAY-BERNE MOLECULES

NVT molecular dynamics simulation are carried out to study the relation between the molecular shape and dipole moment to the liquid crystalline ordering for a system of coupled Gay-Berne molecules. These are dimers of two types of Gay-Berne particles coupled by a harmonic spring. The appearance of the polarisation and biaxiality together with the location of isotropic-nematic clearing temperature are reported for various combinations of position and direction of the dipole attached to the molecule.

Molecular dynamics of cis/ transN-methylformamide liquid mixture using a new optimized all atom rigid force field

The properties of the liquid N-methylformamide (NMF) at normal conditions are studied by means of NVT and NPT molecular dynamics (MD) simulation techniques. The liquid has been modeled for the first time via MD as a mixture of two conformers ( cis and trans) with mole fraction X trans =0.94. A new all atom interaction potential model has been constructed and its reliability in predicting certain properties of the system has been presented. The results obtained reveal the existence of some differences regarding the dynamic and structural properties of the two conformers in the fluid.

Thermodynamic properties and dielectric constants in water/methanol mixtures by integral equation theory and molecular dynamics simulations

A dielectrically adjusted version of the RISM equation for the situation of ions in mixed solvents is applied to model mixtures of water with methanol in concentrations covering the complete concentration range. Calculated structures from the integral equation theory are compared to corresponding results from NVT molecular dynamics simulations. The structure calculated from the integral equation is generally in good agreement with the molecular dynamics results. The agreement in calculated energies between integral equation theory and molecular dynamics simulations are also generally good over the entire concentration range for the specific model applied. For the first time this type of integral equation theory is also applied to the direct calculation of free energy. For the specific water model the free energy is lower than the experimental value for pure water. Under-predictions of the structure and corresponding higher entropy for the specific water model might be one of the reasons for these results. The dielectric constant in a uniform liquid mixture can be described in terms of the dipole moments of the molecules involved and the molecular correlation functions for the different molecular pair combinations in the mixture. In this work I reformulate the theory into a corresponding interaction site formulation. The reformulated theory is illustrated for the water/methanol model mixtures.

CLUSTER GROWTH AND STRUCTURES OF LENNARD-JONES MOLECULES NEAR THE CRITICAL POINT

We considered a two-dimensional system consisting of 529 molecules, interacting with each other via the full Lennard-Jones potential. Using a constant NVT molecular dynamics simulation method, we studied the behavior of this system and analyzed the cluster growth process near the critical point. We considered several data sets near the critical point. By analyzing the cluster formation, we obtained a power law-like behavior for N s (t) , the number of clusters, and S(t) , the average number of molecules in a cluster with respect to time. We also carried out a steady-state analysis. Starting the molecular dynamics simulation in the canonical ensemble, after about 150 ps we changed the ensemble to microcanonical for another approximately 300 ps. We calculated the following static properties: isometric heat capacity, isothermal and adiabatic compressibilities.

The effect of bond length on the structure of dense bead–spring polymer melts

We explored the effect of the ratio of bond length to excluded volume bead diameter, l0/d0, of simple bead–spring homopolymer chains on the resulting liquid structure of dense, monodisperse polymer melts. We conducted NVT molecular dynamics simulations of both bulk and planar confined polymer liquids. We find that both pressure and surface tension increase with l0/d0. We attribute this sensitivity to the reduction in short range liquid ordering, classically observed for simple fluids, when l0/d0<1, and its persistence and even enhancement when l0/d0>1. We explain this by examining specific correlations between bond orientations and monomer density. This leads to a better understanding of how intramolecular constraints influence intermolecular structure in molecular liquids.

DETERMINATION OF THE VAPOR-LIQUID CRITICAL POINT FROM THE SHORT-TIME DYNAMICS

Considering the average potential energy per particle as the parameter, we investigate the early-time dynamics of vapor-liquid transition in the critical region for 2D Lennard-Jones fluids by using NVT molecular dynamics simulations. The results verify the existence of short-time dynamic scaling in the fluid systems and show that the critical point Tc can be determined by the universal short-time behavior. The obtained value of Tc = 0.540 from the short-time dynamics is very close to the value of 0.533 from the Monte Carlo simulations in the equilibrium state of the systems.

Derivation of a general fluid equation of state based on the quasi-Gaussian entropy theory: application to the Lennard-Jones fluid

In this article we present an equation of state for fluids, based on the quasi-Gaussian entropy theory. The temperature dependence along isochores is described by a confined Gamma state, previously introduced, combined with a simple perturbation term. The 11 parameters occurring in the free energy and pressure expressions along the isochores are obtained from molecular dynamics simulation data. The equation of state has been parametrized for the Lennard-Jones fluid in the (reduced) density range 0–1.0 and (reduced) temperature range 1.0–20.0 using (partly new) NVT molecular dynamics simulation data. An excellent agreement for both energy and pressure was obtained. To test the ability to extrapolate to unknown state points, the parametrization was also performed on a smaller set of data in the temperature range 1.0–6.0. The results in the two cases are remarkably close, even in the high temperature range, and are often almost indistinguishable, in contrast to a pure empirical equation of state, like for example the modified Benedict—Webb—Rubin equation. The coexistence line agrees in general very well with Gibbs ensemble and NpT simulation results, and only very close to the critical point there are deviations. Our estimate of the critical point for both parametrizations is somewhat different from the best estimate based on Gibbs ensemble simulations, but is in excellent agreement with other estimates based on NVT simulations and integral equations.

Comparison of Explicit and United Atom Models for Alkane Chains Physisorbed on α-Al2O3 (0001)

Explicit atom (EA) and united atom (UA) models are compared for the description of the structure and dynamics of an alkane film adsorbed on an Al-terminated α-Al2O3 (0001) surface. Ab initio calculations for an Al2O3···CH4 cluster are used to parameterize the EA model. One UA model is derived by explicit averaging of the EA potential, while the second is rescaled from the first to reproduce the EA octane adsorption energy. The appropriate scale factor is found to be sensitive to relaxation of the α-Al2O3 surface. The three models are compared in constant NVT molecular dynamics simulations of an octane monolayer (21 molecules) adsorbed on an 80% relaxed α-Al2O3 (0001) surface. Overall, the UA models reproduce the EA structural predictions well, the primary difference being an underestimation of the average gauche angle and overestimation of the trans fraction in the UA simulations. The agreement between dynamic predictions is less satisfactory; the scaled UA model reproduces the EA trans ↔ gauche interconversion rate reasonably well, but fails to reproduce the overall rotational or translational dynamics. UA models must be used with caution when applied to alkane dynamics on a corrugated surface.

Atomistic simulation and molecular dynamics of model systems for perfluorinated ionomer membranes

An atomistic model for perfluorinated ionomer membranes (PIMs), in particular Nafion materials, is presented and used in conjunction with NVT molecular dynamics simulations to investigate the dynamic and configurational properties of these polymers. It is found that the electrostatic term in the force field is responsible for the formation of an apparently phase separated morphology which is selectively conductive, favouring the passage of cations. Specifically, the mobility of H3O+ ions is found to be ∽3.2 times greater than that of OH- ions, under the application of an external electric field. This phenomenon is shown to be consistent with a jump diffusion model of ion transport in PIMs. There is also evidence for the existence of water in two distinct environments in the simulations: both tightly bound to ion exchange groups, and more loosely associated with the fluorocarbon matrix.

Molecular dynamics simulations and integral equations studies of model systems for aqueous mixtures of small alcohols

In a recent paper (Kvamme (1995)) I suggested a dielectrically adjusted version of the RISM equation for the situation of ions in mixed solvents. In the present work I apply this theory to model mixtures of water with methanol or with ethanol. Calculated structures from the integral equation theory are compared with the corresponding results from NVT molecular dynamics simulations. The results for water + ethanol indicate that the integral equation results are rather sensitive to the short range hydrogen core on methanol. For several of the partial correlation functions the agreement between integral equation theory and molecular dynamics simulations is good. However, unlike the results from molecular simulations, the results from integral equation theory appear to be sensitive to the short range core of the charged hydrogen atoms. A similar type of behaviour is observed in the model system of water and ethanol. Because of this difference in sensitivity of the short range of the charged hydrogens, it is not possible at this stage to draw rigorous conclusions as to the quality of the predictions from the integral equation theory.

Molecular dynamics simulations of PVP kinetic inhibitor in liquid water and hydrate/liquid water systems

The possible effects of PVP (poly(N-vinylpyrrolidone)) on the properties of liquid and water in clathrate hydrate has been investigated using NVT molecular dynamics simulations. A model for a monomer of the PVP polymer is immersed in three systems, liquid water, a unit cell of a hydrate in liquid water with a hydrate former and a third system where some of the liquid water molecules of this last system are replaced by a PVP monomer. Both molecular dynamics simulation and integral equation theory predict hydrogen bonding between the double bonded oxygen in the PVP ring and hydrogens in water. For the composite system, the PVP monomer has a preference for hydrogen bonding to hydrogens from the water molecules at the surface of the hydrate lattice. The simulations indicate that the PVP monomer tends to orient perpendicular to the hydrate surface. For the model systems in this study PVP may form hydrogen bonds with liquid water through the double bonded oxygen in the ring. When a hydrate crystal is immersed i...

Molecular dynamics simulations of PVP kinetic inhibitor in liquid water and hydrate/liquid water systems

The possible effects of PVP (poly(N-vinylpyrrolidone)) on the properties of liquid and water in clathrate hydrate has been investigated using NVT molecular dynamics simulations. A model for a monomer of the PVP polymer is immersed in three systems, liquid water, a unit cell of a hydrate in liquid water with a hydrate former and a third system where some of the liquid water molecules of this last system are replaced by a PVP monomer. Both molecular dynamics simulation and integral equation theory predict hydrogen bonding between the double bonded oxygen in the PVP ring and hydrogens in water. For the composite system, the PVP monomer has a preference for hydrogen bonding to hydrogens from the water molecules at the surface of the hydrate lattice. The simulations indicate that the PVP monomer tends to orient perpendicular to the hydrate surface. For the model systems in this study PVP may form hydrogen bonds with liquid water through the double bonded oxygen in the ring. When a hydrate crystal is immersed in the liquid water phase this hydrogen bonding is shifted towards the hydrate due to a more favourable Coulomb interaction involving hydrogens from more than one water molecule at the hydrate surface. The PVP monomer has a preference for perpendicular orientation with respect to the hydrate surface. A scheme is suggested for the characterization of kinetic hydrate inhibitors based on molecular dynamics simulations and on three basic properties. In addition to the energy between the active groups of the inhibitor and hydrate water another point of focus is the free energy changes in the interactions between the inhibitor and water as the charges are changed from zero to the original model charges. In particular the difference between this integral for the (hydrate water)–(PVP monomer) interaction and the (liquid water)–(PVP inhibitor) interaction should reflect the driving forces in freezing the inhibitor out from the liquid water phase and onto the hydrate surface. The third property in the characterization scheme is the diffusivities of groups connecting to the hydrate crystal, relative to the diffusivities of the hydrate crystal. Results are presented from simulations where a small cavity with a methane model as a guest is immersed in liquid water with free methane molecules at a temperature of 150K. Changes in structure, diffusivities and energy indicate a tendency towards a more solid–like structurde around the cavity.